I had a seam patch on my rear arch, I had the patch put on the inside and then managed to get to the other side by removing the shock and treating it on the other side also. As my cars plain black I just used hamerite and shultz/waxoyl. It's been a year now and no signs of it comming back.
It sounds like you've done the best you can, just keep an eye on it. If you got to both sides then it should be fine IMO.
That was on my driver and the only patch of rust on the whole car, the rest is mint.
Ade